This Article Full Text Full Text (PDF) All Versions of this Article: GR-8730Rv1 13/6a/1203    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Pleasance, E. D. Articles by Jones, S. J.M. Search for Related Content PubMed PubMed Citation Articles by Pleasance, E. D. Articles by Jones, S. J.M. Social Bookmarking                   What's this?

Methods

Assessment of SAGE in Transcript Identification

Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver V5Z 4E6, Canada

An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping are incomplete, and thus do not allow assessment of the efficacy of SAGE in transcript identification. A method of tag mapping is described here and applied to the Drosophila melanogaster and Caenorhabditis elegans genomes, which permits detailed SAGE assessment and provides tag-mapping resources that were unavailable previously for these organisms. In our method, a conceptual transcriptome is constructed using genomic sequence and annotation by extending predicted coding regions to include UTRs on the basis of EST and cDNA alignments, UTR length distributions, and polyadenylation signals. Analysis of extracted tags suggests that, using the standard SAGE procedure, expression of 8% of D. melanogaster and 15% of C. elegans genes cannot be detected unambiguously by SAGE due to shared sequence or lack of NlaIII-anchoring enzyme sites. Both increasing tag length by 2–3 bp and using Sau3A instead of NlaIII as the anchoring enzyme increases potential for transcript detection. This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing tag-to-gene mappings for two model organisms.

Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.873003. Article published online before print in May 2003.

¹ Corresponding author.
E-MAIL sjones{at}bcgsc.bc.ca; FAX (604) 877-6085.

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				P. Huang, E. D. Pleasance, J. S. Maydan, R. Hunt-Newbury, N. J. O'Neil, A. Mah, D. L. Baillie, M. A. Marra, D. G. Moerman, and S. J.M. Jones Identification and analysis of internal promoters in Caenorhabditis elegans operons Genome Res., October 1, 2007; 17(10): 1478 - 1485. [Abstract] [Full Text] [PDF]

				M. Metta, R. Gudavalli, J.-M. Gibert, and C. Schlotterer No Accelerated Rate of Protein Evolution in Male-Biased Drosophila pseudoobscura Genes Genetics, September 1, 2006; 174(1): 411 - 420. [Abstract] [Full Text] [PDF]

				S. LEE, J. BAO, G. ZHOU, J. SHAPIRO, J. XU, R. Z. SHI, X. LU, T. CLARK, D. JOHNSON, Y. C. KIM, et al. Detecting novel low-abundant transcripts in Drosophila RNA, June 1, 2005; 11(6): 939 - 946. [Abstract] [Full Text] [PDF]

				J. Halaschek-Wiener, J. S. Khattra, S. McKay, A. Pouzyrev, J. M. Stott, G. S. Yang, R. A. Holt, S. J.M. Jones, M. A. Marra, A. R. Brooks-Wilson, et al. Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression Genome Res., May 1, 2005; 15(5): 603 - 615. [Abstract] [Full Text] [PDF]

				M. B. Wahl, U. Heinzmann, and K. Imai LongSAGE analysis significantly improves genome annotation: identifications of novel genes and alternative transcripts in the mouse Bioinformatics, April 15, 2005; 21(8): 1393 - 1400. [Abstract] [Full Text] [PDF]

				S. J. Robinson, D. J. Cram, C. T. Lewis, and I. A.P. Parkin Maximizing the Efficacy of SAGE Analysis Identifies Novel Transcripts in Arabidopsis Plant Physiology, October 1, 2004; 136(2): 3223 - 3233. [Abstract] [Full Text] [PDF]

				B. J. Hwang, H.-M. Muller, and P. W. Sternberg Genome annotation by high-throughput 5' RNA end determination PNAS, February 10, 2004; 101(6): 1650 - 1655. [Abstract] [Full Text] [PDF]

				C. Fizames, S. Munos, C. Cazettes, P. Nacry, J. Boucherez, F. Gaymard, D. Piquemal, V. Delorme, T. Commes, P. Doumas, et al. The Arabidopsis Root Transcriptome by Serial Analysis of Gene Expression. Gene Identification Using the Genome Sequence Plant Physiology, January 1, 2004; 134(1): 67 - 80. [Abstract] [Full Text] [PDF]

				H. Matsumura, S. Reich, A. Ito, H. Saitoh, S. Kamoun, P. Winter, G. Kahl, M. Reuter, D. H. Kruger, and R. Terauchi Gene expression analysis of plant host-pathogen interactions by SuperSAGE PNAS, December 23, 2003; 100(26): 15718 - 15723. [Abstract] [Full Text] [PDF]